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Arabidopsis thaliana vs Trifolium pratense LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Trifolium pratense (Trifolium pratense, Trpr) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterArabidopsis thalianaTrifolium pratense
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 146,024 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 83,379,556 out of 119,667,750
Covered: 36,288,194 out of 119,667,750

Uncovered: 9,228,356 out of 33,775,569
Matches: 15,981,393 out of 33,775,569
Mismatches: 8,005,421 out of 33,775,569
Insertions: 560,399 out of 33,775,569
Identity over aligned base-pairs: 65.1%

Trifolium pratense

Uncovered: 262,307,365 out of 304,842,038
Covered: 42,534,673 out of 304,842,038

Uncovered: 15,071,704 out of 41,242,947
Matches: 17,364,740 out of 41,242,947
Mismatches: 8,113,715 out of 41,242,947
Insertions: 692,788 out of 41,242,947
Identity over aligned base-pairs: 66.4%

Block size distribution

Size range All 146,024 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,351
7.5 kb
10 bp - 100 bp
21,020
1.4 Mb
4,547
322.0 kb
100 bp - 1 kb
112,877
39.0 Mb
29,356
11.8 Mb
1 kb - 10 kb
10,736
16.7 Mb
17,858
41.5 Mb
10 kb - 100 kb
40
416.6 kb
274
3.8 Mb